21 Jun 2021 19:49:31,877 INFO : Copying experiment "Validation of proteins showing significant dysregulation from shotgun proteomics experiments in longitudinal plasma samples of COVID-19 patients" from folder /IIT Bombay - Proteomics/Longitudinal plasma MRM to /Panorama Public/2021/IIT Bombay Proteomics - Longitudinal plasma MRM
21 Jun 2021 19:49:31,877 INFO : =======================================
21 Jun 2021 19:49:31,941 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
21 Jun 2021 19:49:31,942 INFO :
21 Jun 2021 19:49:31,943 INFO : Exporting experiment.
21 Jun 2021 19:49:49,389 INFO :
21 Jun 2021 19:49:49,389 INFO : Experiment export completed successfully.
21 Jun 2021 19:49:49,390 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
21 Jun 2021 19:49:49,419 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
21 Jun 2021 19:49:49,419 INFO :
21 Jun 2021 19:49:49,419 INFO : Importing experiment.
21 Jun 2021 19:49:49,423 INFO : Loading folder properties (folder type, settings and active modules)
21 Jun 2021 19:49:49,501 INFO : Done importing folder properties (folder type, settings and active modules)
21 Jun 2021 19:49:49,503 INFO : Loading etl definitions
21 Jun 2021 19:49:49,505 INFO : Loading wikis
21 Jun 2021 19:49:49,507 INFO : 0 wikis imported
21 Jun 2021 19:49:49,507 INFO : Done importing wikis
21 Jun 2021 19:49:49,507 INFO : Starting to copy files
21 Jun 2021 19:49:53,715 INFO : Copied 25 files
21 Jun 2021 19:49:53,716 INFO : Ensuring exp.data rows exist for imported files
21 Jun 2021 19:49:53,868 INFO : Starting Sample Type and Data Class import
21 Jun 2021 19:49:53,869 INFO : No types XAR file to process.
21 Jun 2021 19:49:53,869 INFO : Finished importing Sample Types and Data Classes
21 Jun 2021 19:49:53,871 INFO : Loading xar
21 Jun 2021 19:49:55,357 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8743:TargetedMS.ImportSkyZip'
21 Jun 2021 19:49:55,359 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8743:TargetedMS.ImportSkyZip.Core'
21 Jun 2021 19:49:55,362 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8743:TargetedMS.ImportSkyZip.Output'
21 Jun 2021 19:49:55,362 DEBUG: Protocol import complete
21 Jun 2021 19:49:55,364 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-8743:Validation+of+proteins+showing+significant+dysregulation+from+shotgun+proteomics+experiments+in+longitudinal+plasma+samples+of+COVID-19+patients'
21 Jun 2021 19:49:55,364 DEBUG: Experiment/Run group import complete
21 Jun 2021 19:49:55,373 DEBUG: Protocol action set import complete
21 Jun 2021 19:49:55,392 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8743:TargetedMS.ImportSkyZip'
21 Jun 2021 19:49:55,400 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-8743:3171dc22-b247-1039-be5b-fea6ddf5138a'
21 Jun 2021 19:49:55,404 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-8743:3171dbe7-b247-1039-be5b-fea6ddf5138a'
21 Jun 2021 19:49:55,404 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8743:TargetedMS.ImportSkyZip.Core'
21 Jun 2021 19:49:55,406 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8743:TargetedMS.ImportSkyZip.Output'
21 Jun 2021 19:49:55,407 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-8743:3171dc6b-b247-1039-be5b-fea6ddf5138a'
21 Jun 2021 19:49:55,408 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20Longitudinal%20plasma%20MRM_3f7f13ce-b531-1039-be5b-fea6ddf5138a/_temp__2021-06-21_19-49-31/export/xar/experiments_and_runs.xar.exploded/Run111741/Longitudinal_plasma_MRM_2021-06-18_15-14-52/Longitudinal_plasma_MRM.skyd into the system
21 Jun 2021 19:49:55,409 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20Longitudinal%20plasma%20MRM_3f7f13ce-b531-1039-be5b-fea6ddf5138a/_temp__2021-06-21_19-49-31/export/xar/experiments_and_runs.xar.exploded/Run111741/Longitudinal_plasma_MRM_2021-06-18_15-14-52/Longitudinal_plasma_MRM.skyd into the system
21 Jun 2021 19:49:55,409 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20Longitudinal%20plasma%20MRM_3f7f13ce-b531-1039-be5b-fea6ddf5138a/_temp__2021-06-21_19-49-31/export/xar/experiments_and_runs.xar.exploded/Run111741/Longitudinal_plasma_MRM_2021-06-18_15-14-52.sky.zip into the system
21 Jun 2021 19:49:55,410 INFO : Starting import from Longitudinal_plasma_MRM_2021-06-18_15-14-52.sky.zip
21 Jun 2021 19:49:55,415 INFO : Starting to import Skyline document from Longitudinal_plasma_MRM_2021-06-18_15-14-52.sky.zip
21 Jun 2021 19:49:55,415 INFO : Expanding Human.protdb
21 Jun 2021 19:49:58,209 INFO : Expanding Longitudinal_plasma_MRM.skyd
21 Jun 2021 19:49:58,218 INFO : Expanding Longitudinal_plasma_MRM.sky.view
21 Jun 2021 19:49:58,218 INFO : Expanding Longitudinal_plasma_MRM.sky
21 Jun 2021 19:49:58,219 INFO : Expanding Longitudinal_plasma_MRM.skyl
21 Jun 2021 19:49:58,226 WARN : The version of this Skyline document is 21.1. This is newer than the highest supported version 20.2
21 Jun 2021 19:49:58,233 INFO : 6% Done
21 Jun 2021 19:49:58,254 DEBUG: Starting to load chromatogram headers
21 Jun 2021 19:49:58,254 DEBUG: Done loading chromatogram headers
21 Jun 2021 19:49:58,289 INFO : Inserting sp|P02774|VTDB_HUMAN
21 Jun 2021 19:49:58,294 INFO : 12% Done
21 Jun 2021 19:49:58,314 INFO : 21% Done
21 Jun 2021 19:49:58,331 INFO : 31% Done
21 Jun 2021 19:49:58,345 DEBUG: Total peptides inserted: 3
21 Jun 2021 19:49:58,350 INFO : Inserting sp|P07737|PROF1_HUMAN
21 Jun 2021 19:49:58,355 INFO : 43% Done
21 Jun 2021 19:49:58,375 INFO : 54% Done
21 Jun 2021 19:49:58,392 INFO : 62% Done
21 Jun 2021 19:49:58,406 DEBUG: Total peptides inserted: 3
21 Jun 2021 19:49:58,407 INFO : Inserting peptides1
21 Jun 2021 19:49:58,413 INFO : 80% Done
21 Jun 2021 19:49:58,438 DEBUG: Total peptides inserted: 1
21 Jun 2021 19:49:58,438 INFO : Done parsing Skyline document.
21 Jun 2021 19:49:58,441 INFO : Calculating fold changes
21 Jun 2021 19:49:58,441 DEBUG: Calculating fold change for group comparison T1 vs T2, 1 of 1
21 Jun 2021 19:49:58,528 INFO : 98% Done
21 Jun 2021 19:49:58,528 INFO : Done calculating fold changes.
21 Jun 2021 19:50:02,159 INFO : Creating and populating temp tables for Proportion values
21 Jun 2021 19:50:02,168 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
21 Jun 2021 19:50:02,173 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
21 Jun 2021 19:50:02,178 INFO : Cleaning up temp tables
21 Jun 2021 19:50:02,454 INFO : Completed import of Skyline document from Longitudinal_plasma_MRM_2021-06-18_15-14-52.sky.zip
21 Jun 2021 19:50:02,457 INFO : 100% Done
21 Jun 2021 19:50:02,462 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20Longitudinal%20plasma%20MRM_3f7f13ce-b531-1039-be5b-fea6ddf5138a/_temp__2021-06-21_19-49-31/export/xar/experiments_and_runs.xar.exploded/Run111741/Longitudinal_plasma_MRM_2021-06-18_15-14-52.sky.zip into the system
21 Jun 2021 19:50:02,469 INFO : Done importing xar
21 Jun 2021 19:50:02,471 INFO : Loading pages and webpart properties
21 Jun 2021 19:50:02,533 INFO : Done importing pages and webpart properties
21 Jun 2021 19:50:02,534 INFO :
21 Jun 2021 19:50:02,534 INFO : Experiment import completed successfully.
21 Jun 2021 19:50:02,534 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
21 Jun 2021 19:50:02,563 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
21 Jun 2021 19:50:02,563 INFO :
21 Jun 2021 19:50:02,564 INFO : Finishing up experiment copy.
21 Jun 2021 19:50:02,564 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
21 Jun 2021 19:50:02,566 INFO : Assigning a ProteomeXchange ID.
21 Jun 2021 19:50:02,741 INFO : Assigning a DOI.
21 Jun 2021 19:50:03,744 INFO : Assigned DOI: 10.6069/bf55-2520
21 Jun 2021 19:50:03,747 INFO : Updating access URL to point to the new copy of the data.
21 Jun 2021 19:50:03,750 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
21 Jun 2021 19:50:03,751 INFO : Removing copy permissions given to journal.
21 Jun 2021 19:50:03,768 INFO : Adding read permissions to all users that are folder admins in the source container.
21 Jun 2021 19:50:03,775 INFO : Setting the TargetedMS folder type to 'Experimental Data'
21 Jun 2021 19:50:03,784 INFO : Updating the 'Raw Data' tab configuration
21 Jun 2021 19:50:03,787 INFO : Updating dataFileUrls for run Longitudinal_plasma_MRM_2021-06-18_15-14-52.sky.zip; targetedms run ID 114168
21 Jun 2021 19:50:03,788 INFO : Updating dataFileUrl...
21 Jun 2021 19:50:03,788 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20Longitudinal%20plasma%20MRM_3f7f13ce-b531-1039-be5b-fea6ddf5138a/_temp__2021-06-21_19-49-31/export/xar/experiments_and_runs.xar.exploded/Run111741/Longitudinal_plasma_MRM_2021-06-18_15-14-52.sky.zip
21 Jun 2021 19:50:03,788 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/IIT%20Bombay%20Proteomics%20-%20Longitudinal%20plasma%20MRM/@files/Longitudinal_plasma_MRM_2021-06-18_15-14-52.sky.zip
21 Jun 2021 19:50:03,792 INFO : Updating dataFileUrl...
21 Jun 2021 19:50:03,793 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20Longitudinal%20plasma%20MRM_3f7f13ce-b531-1039-be5b-fea6ddf5138a/_temp__2021-06-21_19-49-31/export/xar/experiments_and_runs.xar.exploded/Run111741/Longitudinal_plasma_MRM_2021-06-18_15-14-52/Longitudinal_plasma_MRM.skyd
21 Jun 2021 19:50:03,793 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/IIT%20Bombay%20Proteomics%20-%20Longitudinal%20plasma%20MRM/@files/Longitudinal_plasma_MRM_2021-06-18_15-14-52/Longitudinal_plasma_MRM.skyd
21 Jun 2021 19:50:03,795 INFO : Creating a reviewer account.
21 Jun 2021 19:50:04,007 INFO : Created reviewer with email: User panorama+reviewer39@proteinms.net
21 Jun 2021 19:50:04,017 INFO : Hiding the Data Pipeline tab.
21 Jun 2021 19:50:04,100 INFO : Emailing submitter.
21 Jun 2021 19:50:04,227 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'